Skip to main content

Understanding Thermostability Factors of Aspergillus niger PhyA Phytase: A Molecular Dynamics Study

Abstract

Molecular dynamics simulation was used to study the dynamic differences between native Aspergillus niger PhyA phytase and a mutant with 20 % greater thermostability. Atomic root mean square deviation, radius of gyration, and number of hydrogen bonds and salt bridges are examined to determine thermostability factors. The results suggest that, among secondary structure elements, loops have the most impact on the thermal stability of A. niger phytase. In addition, the location rather than the number of hydrogen bonds is found to have an important contribution to thermostability. The results also show that salt bridges may have stabilizing or destabilizing effect on the enzyme and influence its thermostability accordingly.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Abbreviations

MD:

Molecular dynamics

ANP:

Aspergillus niger phytase

mANP:

Mutant Aspergillus niger phytase

RMSD:

Root mean square deviation

RMSF:

Root mean square fluctuation

R g :

Radius of gyration

References

  1. Barakat NH, Barakat NH, Love JJ (2010) Protein Eng Des Sel 23:799–807

    Article  CAS  Google Scholar 

  2. Berman H, Westbrook MJ, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235–242

    Article  CAS  Google Scholar 

  3. Bogin O, Levin I, Tel-Or S, Peretz M, Frolow F, Burstein Y (2002) Protein Sci 11:2561–2574

    Article  CAS  Google Scholar 

  4. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comput Chem 4:187–217

    Article  CAS  Google Scholar 

  5. Chakravarty S, Varadarajan R (2000) FEBS Lett 470:65–69

    Article  CAS  Google Scholar 

  6. Dalhus B, Saarinen M, Sauer UH, Eklund P, Johansson K, Karlsson A, Ramaswamy S, Bjork A, Synstad B, Naterstad K, Sirevag R, Eklund H (2002) J Mol Biol 318:707–721

    Article  CAS  Google Scholar 

  7. Darden T, York D, Pederson L (1993) J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  8. Fei B, Xu H, Zhang F, Li X, Ma S, Cao Y, Xie J, Qiao D, Cao Y (2012) J Biosci Bioeng. doi:10.1016/j.jbiosc.2012.12.010

  9. Fletcher R, Reeves CM (1964) Comput J 7:149–154

    Article  Google Scholar 

  10. Greiner R, Farouk AE (2007) Protein J 26:577–584

    Article  CAS  Google Scholar 

  11. Greiner R, Konietzny U (2006) Food Technol Biotechnol 44:125–140

    CAS  Google Scholar 

  12. Haefner S, Knietsch A, Scholten E, Braun J, Lohscheidt M, Zelder O (2005) Appl Microbiol Biotechnol 68:588–597

    Article  CAS  Google Scholar 

  13. Han Y, Wilson DB, Lei XG (1999) Appl Environ Microbiol 65:1915–1918

    CAS  Google Scholar 

  14. Humphrey W, Dalke A, Schulten K (1996) J Molec Graph 14:33–38

    Article  CAS  Google Scholar 

  15. Jermutus L, Tessier M, Pasamontes L, van Loon APGM, Lehmann M (2001) J Biotechnol 85:15–24

    Article  CAS  Google Scholar 

  16. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  17. Karplus M, McCammon JA (2002) Nature Struct Biol 9:646–652

    Article  CAS  Google Scholar 

  18. Karshikoff A, Ladenstein R (1998) Protein Eng 11:867–872

    Article  CAS  Google Scholar 

  19. Kim MS, Lei XG (2008) Appl Microbiol Biotechnol 79:69–75

    Article  CAS  Google Scholar 

  20. Kim MS, Weaver JD, Lei XG (2008) Appl Microbiol Biotechnol 79:751–758

    Article  CAS  Google Scholar 

  21. Kim YW, Choi JH, Kim JW, Park C, Kim JW, Cha H, Lee SB, Oh BH, Moon TW, Park KH (2003) Appl Environ Microbiol 69:4866–4874

    Article  CAS  Google Scholar 

  22. Konietzny U, Greiner R (2002) Int J Food Sci Technol 37:791–812

    Article  CAS  Google Scholar 

  23. Konietzny U, Greiner R (2004) Braz J Microbiol 35:11–18

    Article  CAS  Google Scholar 

  24. Kumar S, Nussinov R (2001) Cell Mol Life Sci 58:1216–1233

    Article  CAS  Google Scholar 

  25. Lehmann M, Kostrewa D, Wyss M, Brugger R, D’Arcy A, Pasamontes L, van Loon APGM (2000) Protein Eng 13:49–57

    Article  CAS  Google Scholar 

  26. Lehmann M, Loch C, Middendorf A, Studer D, Lassen SF, Pasamontes L, van Loon AP, Wyss M (2002) Protein Eng 15:403–411

    Article  CAS  Google Scholar 

  27. Lehmann M, Lopez-Ulibarri R, Loch C, Viarouge C, Wyss M, van Loon APGM (2000) Protein Sci 9:1866–1872

    Article  CAS  Google Scholar 

  28. Lei XG, Porres JM (2003) Biotechnol Lett 25:1787–1794

    Article  CAS  Google Scholar 

  29. Lu T (2009) Chem Phys Lett 477:202–206

    Article  CAS  Google Scholar 

  30. Milardi D, Pappalardo M, Pannuzzo M, Grasso DM, Rosa CL (2008) Chem Phys Lett 463:396–399

    Article  CAS  Google Scholar 

  31. Oakley AJ (2010) Biochem Biophys Res Commun 397:745–749

    Article  CAS  Google Scholar 

  32. Oh BC, Choi WC, Park S, Kim YO, Oh TK (2004) Appl Microbiol Biotechnol 63:362–372

    Article  CAS  Google Scholar 

  33. Pedretti A, Villa L, Vistoli G (2002) J Mol Graph 21:47–49

    Article  CAS  Google Scholar 

  34. Phillips JC (2005) J Comput Chem 26:1781–1802

    Article  CAS  Google Scholar 

  35. Purmonen M, Valjakka J, Takkinen K, Laitinen T, Rouvinen J (2007) Protein Eng Des Sel 20:551–559

    Article  CAS  Google Scholar 

  36. Szilagyi A, Zavodszky P (2000) Structure 8:493–504

    Article  CAS  Google Scholar 

  37. Vats P, Banerjee UC (2004) Enzyme Microb Technol 35:3–14

    Article  CAS  Google Scholar 

  38. Vieille C, Zeikus GJ (2001) Microbiol Mol Biol R 65:1–43

    Article  CAS  Google Scholar 

  39. Vogt G, Argos P (1997) Fold Des 2:S40–S46

    Article  CAS  Google Scholar 

  40. Vogt G, Woell S, Argos P (1997) J Mol Biol 269:631–643

    Article  CAS  Google Scholar 

  41. Voigt CA, Mayo SL, Arnold FH, Wang ZG (2001) PNAS 98:3778–3783

    Article  CAS  Google Scholar 

  42. Williams JC, Zeelen JP, Neubauer G, Vriend G, Backmann J, Michels PAM, Lambeir AM, Wierenga RK (1999) Protein Eng 12:243–250

    Article  CAS  Google Scholar 

  43. Xiang T, Liu Q, Deacon AM, Koshy M, Kriksunov IA, Lei XG, Hao Q, Thiel DJ (2004) J Mol Biol 339:437–445

    Article  CAS  Google Scholar 

  44. Zhang W, Lei XG (2008) Appl Microbiol Biotechnol 77:1033–1040

    Article  CAS  Google Scholar 

  45. Zhang W, Mullaney EJ, Lei XG (2007) Appl Environ Microbiol 73:3069–3076

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to I. A. Noorbatcha.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Noorbatcha, I.A., Sultan, A.M., Salleh, H.M. et al. Understanding Thermostability Factors of Aspergillus niger PhyA Phytase: A Molecular Dynamics Study. Protein J 32, 309–316 (2013). https://doi.org/10.1007/s10930-013-9489-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10930-013-9489-y

Keywords